Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Generation of Orchard and Tree-Child Networks
Bull Math Biol. 2023 Dec 20;86(1):10. doi: 10.1007/s11538-023-01239-z.ABSTRACTPhylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are d...
Source: Bulletin of Mathematical Biology - December 20, 2023 Category: Bioinformatics Authors: Gabriel Cardona Gerard Ribas Joan Carles Pons Source Type: research
Dynamics of a Mosquito Egg-Larvae Model with Seasonality
Bull Math Biol. 2023 Dec 18;86(1):9. doi: 10.1007/s11538-023-01238-0.ABSTRACTWe propose a two stages mosquito egg-larvae model with seasonality as a simplification of a four stages one. For the simplified model we characterize the dynamics in terms of the vectorial reproduction number, [Formula: see text], obtaining extinction if [Formula: see text] and convergence to a unique positive periodic orbit if [Formula: see text]. We illustrate each case with an example, by providing general conditions on the periodic coefficients for its occurrence. These examples are further developed using numerical simulations where the perio...
Source: Bulletin of Mathematical Biology - December 18, 2023 Category: Bioinformatics Authors: Jes ús Bellver-Arnau Alessandro Margheri Carlota Rebelo Source Type: research
Dynamics of a Mosquito Egg-Larvae Model with Seasonality
Bull Math Biol. 2023 Dec 18;86(1):9. doi: 10.1007/s11538-023-01238-0.ABSTRACTWe propose a two stages mosquito egg-larvae model with seasonality as a simplification of a four stages one. For the simplified model we characterize the dynamics in terms of the vectorial reproduction number, [Formula: see text], obtaining extinction if [Formula: see text] and convergence to a unique positive periodic orbit if [Formula: see text]. We illustrate each case with an example, by providing general conditions on the periodic coefficients for its occurrence. These examples are further developed using numerical simulations where the perio...
Source: Bulletin of Mathematical Biology - December 18, 2023 Category: Bioinformatics Authors: Jes ús Bellver-Arnau Alessandro Margheri Carlota Rebelo Source Type: research
Models for Implant-Induced Capsular Contracture Post Breast Cancer Surgery
Bull Math Biol. 2023 Dec 13;86(1):7. doi: 10.1007/s11538-023-01236-2.ABSTRACTCapsular contracture is a painful deformation of scar-tissue that may form around an implant in post-breast cancer reconstruction or cosmetic surgery. Inflammation due to surgical trauma or contamination in the tissue around the implant could account for recruitment of immune cells, and transdifferentiation of resident fibroblasts into cells that deposit abnormally thick collagen. Here we examine this hypothesis using a mathematical model for interacting macrophages, fibroblasts, myofibroblasts, and collagen. Our model demonstrates that cellular r...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Cheryl Dyck Kathryn V Isaac Leah Edelstein-Keshet Source Type: research
Formation and Growth of Co-Culture Tumour Spheroids: New Compartment-Based Mathematical Models and Experiments
Bull Math Biol. 2023 Dec 13;86(1):8. doi: 10.1007/s11538-023-01229-1.ABSTRACTCo-culture tumour spheroid experiments are routinely performed to investigate cancer progression and test anti-cancer therapies. Therefore, methods to quantitatively characterise and interpret co-culture spheroid growth are of great interest. However, co-culture spheroid growth is complex. Multiple biological processes occur on overlapping timescales and different cell types within the spheroid may have different characteristics, such as differing proliferation rates or responses to nutrient availability. At present there is no standard, widely-ac...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Ryan J Murphy Gency Gunasingh Nikolas K Haass Matthew J Simpson Source Type: research
Models for Implant-Induced Capsular Contracture Post Breast Cancer Surgery
Bull Math Biol. 2023 Dec 13;86(1):7. doi: 10.1007/s11538-023-01236-2.ABSTRACTCapsular contracture is a painful deformation of scar-tissue that may form around an implant in post-breast cancer reconstruction or cosmetic surgery. Inflammation due to surgical trauma or contamination in the tissue around the implant could account for recruitment of immune cells, and transdifferentiation of resident fibroblasts into cells that deposit abnormally thick collagen. Here we examine this hypothesis using a mathematical model for interacting macrophages, fibroblasts, myofibroblasts, and collagen. Our model demonstrates that cellular r...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Cheryl Dyck Kathryn V Isaac Leah Edelstein-Keshet Source Type: research
Formation and Growth of Co-Culture Tumour Spheroids: New Compartment-Based Mathematical Models and Experiments
Bull Math Biol. 2023 Dec 13;86(1):8. doi: 10.1007/s11538-023-01229-1.ABSTRACTCo-culture tumour spheroid experiments are routinely performed to investigate cancer progression and test anti-cancer therapies. Therefore, methods to quantitatively characterise and interpret co-culture spheroid growth are of great interest. However, co-culture spheroid growth is complex. Multiple biological processes occur on overlapping timescales and different cell types within the spheroid may have different characteristics, such as differing proliferation rates or responses to nutrient availability. At present there is no standard, widely-ac...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Ryan J Murphy Gency Gunasingh Nikolas K Haass Matthew J Simpson Source Type: research
Models for Implant-Induced Capsular Contracture Post Breast Cancer Surgery
Bull Math Biol. 2023 Dec 13;86(1):7. doi: 10.1007/s11538-023-01236-2.ABSTRACTCapsular contracture is a painful deformation of scar-tissue that may form around an implant in post-breast cancer reconstruction or cosmetic surgery. Inflammation due to surgical trauma or contamination in the tissue around the implant could account for recruitment of immune cells, and transdifferentiation of resident fibroblasts into cells that deposit abnormally thick collagen. Here we examine this hypothesis using a mathematical model for interacting macrophages, fibroblasts, myofibroblasts, and collagen. Our model demonstrates that cellular r...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Cheryl Dyck Kathryn V Isaac Leah Edelstein-Keshet Source Type: research
Formation and Growth of Co-Culture Tumour Spheroids: New Compartment-Based Mathematical Models and Experiments
Bull Math Biol. 2023 Dec 13;86(1):8. doi: 10.1007/s11538-023-01229-1.ABSTRACTCo-culture tumour spheroid experiments are routinely performed to investigate cancer progression and test anti-cancer therapies. Therefore, methods to quantitatively characterise and interpret co-culture spheroid growth are of great interest. However, co-culture spheroid growth is complex. Multiple biological processes occur on overlapping timescales and different cell types within the spheroid may have different characteristics, such as differing proliferation rates or responses to nutrient availability. At present there is no standard, widely-ac...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Ryan J Murphy Gency Gunasingh Nikolas K Haass Matthew J Simpson Source Type: research
Models for Implant-Induced Capsular Contracture Post Breast Cancer Surgery
Bull Math Biol. 2023 Dec 13;86(1):7. doi: 10.1007/s11538-023-01236-2.ABSTRACTCapsular contracture is a painful deformation of scar-tissue that may form around an implant in post-breast cancer reconstruction or cosmetic surgery. Inflammation due to surgical trauma or contamination in the tissue around the implant could account for recruitment of immune cells, and transdifferentiation of resident fibroblasts into cells that deposit abnormally thick collagen. Here we examine this hypothesis using a mathematical model for interacting macrophages, fibroblasts, myofibroblasts, and collagen. Our model demonstrates that cellular r...
Source: Bulletin of Mathematical Biology - December 13, 2023 Category: Bioinformatics Authors: Cheryl Dyck Kathryn V Isaac Leah Edelstein-Keshet Source Type: research
